Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 7026373 Shewana3_3515 ABC transporter related (RefSeq)
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__ANA3:7026373 Length = 349 Score = 187 bits (475), Expect = 4e-52 Identities = 106/272 (38%), Positives = 163/272 (59%), Gaps = 9/272 (3%) Query: 21 LDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRLVASNGKLIVPPE 80 L +++ + GE +LGPSG GKTT +R +AGL S GE+ + + V+ G+ VP E Sbjct: 20 LKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGEIQINGKTVSGAGQF-VPSE 78 Query: 81 DRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKILDIHHVLNHFPRE 140 R IGM+FQ +AL+P+LT ENI F + K++ + + R++++ ++ + + +P E Sbjct: 79 QRGIGMIFQDYALFPHLTVAENILFGVA--KLTPAQRKARLDDMLALVKLEGLAKRYPHE 136 Query: 141 LSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGVTLLVVSHD 200 LSGGQQQRV++ARAL +P LLLLDEPFSN+DA++R S A ++ + + V+ + V+H Sbjct: 137 LSGGQQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMMAEIRSILKQRNVSAVFVTHS 196 Query: 201 PADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINELEGKVTNEGVV--- 257 + F AD + + +G +VQ G+ E+LY P S VA +G N L +V + V Sbjct: 197 KDEAFVFADTLAIFNQGVIVQHGRAENLYAAPNSRYVADFLGSGNYLPAEVIDGHSVVTP 256 Query: 258 IGSLRFPVSVSSDRAIIG---IRPEDVKLSKD 286 IG LR +S A G +RP+ + LS D Sbjct: 257 IGELRSLTPLSQSHAFNGQVFLRPQQLALSAD 288 Lambda K H 0.319 0.139 0.390 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 255 Number of extensions: 8 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 353 Length of database: 349 Length adjustment: 29 Effective length of query: 324 Effective length of database: 320 Effective search space: 103680 Effective search space used: 103680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory